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Sun W, Wang Z, Wen S, Huang A, Li H, Jiang L, Feng Q, Fan D, Tian Q, Han D, Liu X. Technical strategy for monozygotic twin discrimination by single-nucleotide variants. Int J Legal Med 2024; 138:767-779. [PMID: 38197923 DOI: 10.1007/s00414-023-03150-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 12/11/2023] [Indexed: 01/11/2024]
Abstract
Monozygotic (MZ) twins are theoretically genetically identical. Although they are revealed to accumulate mutations after the zygote splits, discriminating between twin genomes remains a formidable challenge in the field of forensic genetics. Single-nucleotide variants (SNVs) are responsible for a substantial portion of genetic variation, thus potentially serving as promising biomarkers for the identification of MZ twins. In this study, we sequenced the whole genome of a pair of female MZ twins when they were 27 and 33 years old to approximately 30 × coverage using peripheral blood on an Illumina NovaSeq 6000 Sequencing System. Potentially discordant SNVs supported by whole-genome sequencing were validated extensively by amplicon-based targeted deep sequencing and Sanger sequencing. In total, we found nine bona fide post-twinning SNVs, all of which were identified in the younger genomes and found in the older genomes. None of the SNVs occurred within coding exons, three of which were observed in introns, supported by whole-exome sequencing results. A double-blind test was employed, and the reliability of MZ twin discrimination by discordant SNVs was endorsed. All SNVs were successfully detected when input DNA amounts decreased to 0.25 ng, and reliable detection was limited to seven SNVs below 0.075 ng input. This comprehensive analysis confirms that SNVs could serve as cost-effective biomarkers for MZ twin discrimination.
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Affiliation(s)
- Weifen Sun
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Ministry of Justice, Shanghai, 200063, China
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Ziwei Wang
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Ministry of Justice, Shanghai, 200063, China
- Department of Forensic Science, Medical School of Soochow University, Suzhou, 215123, China
| | - Shubo Wen
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Ministry of Justice, Shanghai, 200063, China
- Department of Forensic Science, Medical School of Soochow University, Suzhou, 215123, China
| | - Ao Huang
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Ministry of Justice, Shanghai, 200063, China
- Department of Forensic Science, Medical School of Soochow University, Suzhou, 215123, China
| | - Hui Li
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Ministry of Justice, Shanghai, 200063, China
| | - Lei Jiang
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Ministry of Justice, Shanghai, 200063, China
| | - Qi Feng
- National Center for Gene Research, State Key Laboratory of Plant Molecular Genetics, Center of Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200233, China
| | - Danlin Fan
- National Center for Gene Research, State Key Laboratory of Plant Molecular Genetics, Center of Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200233, China
| | - Qilin Tian
- National Center for Gene Research, State Key Laboratory of Plant Molecular Genetics, Center of Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200233, China
| | - Dingding Han
- Department of Clinical Laboratory, Shanghai Children's Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200062, China
| | - Xiling Liu
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Ministry of Justice, Shanghai, 200063, China.
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2
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Yang Z, Yang J, Yue L, Shen B, Wang J, Miao Y, Ouyang R, Hu Y. Enhancement Effects and Mechanism Studies of Two Bismuth-Based Materials Assisted by DMSO and Glycerol in GC-Rich PCR. Molecules 2023; 28:molecules28114515. [PMID: 37298991 DOI: 10.3390/molecules28114515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 04/22/2023] [Accepted: 04/30/2023] [Indexed: 06/12/2023] Open
Abstract
Polymerase chain reaction (PCR) has extensive bioanalytical applications in molecular diagnostics and genomic research studies for rapid detection and precise genomic amplification. Routine integrations for analytical workflow indicate certain limitations, including low specificity, efficiency, and sensitivity in conventional PCR, particularly towards amplifying high guanine-cytosine (GC) content. Further, there are many ways to enhance the reaction, for example, using different PCR strategies such as hot-start/touchdown PCR or adding some special modifications or additives such as organic solvents or compatible solutes, which can improve PCR yield. Due to the widespread use of bismuth-based materials in biomedicine, which have not yet been used for PCR optimization, this attracts our attention. In this study, two bismuth-based materials that are inexpensive and readily available were used to optimize GC-rich PCR. The results demonstrated that ammonium bismuth citrate and bismuth subcarbonate effectively enhanced PCR amplification of the GNAS1 promoter region (∼84% GC) and APOE (75.5% GC) gene of Homo sapiens mediated by Ex Taq DNA polymerase within the appropriate concentration range. Combining DMSO and glycerol additives was critical in obtaining the target amplicons. Thus, the solvents mixed with 3% DMSO and 5% glycerol were used in bismuth-based materials. That allowed for better dispersion of bismuth subcarbonate. As for the enhanced mechanisms, the surface interaction of PCR components, including Taq polymerase, primer, and products with bismuth-based materials, was maybe the main reason. The addition of materials can reduce the melting temperature (Tm), adsorb polymerase and modulate the amount of active polymerase in PCR, facilize the dissociation of DNA products, and enhance the specificity and efficiency of PCR. This work provided a class of candidate enhancers for PCR, deepened our understanding of the enhancement mechanisms of PCR, and also explored a new application field for bismuth-based materials.
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Affiliation(s)
- Zhu Yang
- Institute of Bismuth and Rhenium Science, School Materials and Chemistry, University of Shanghai for Science and Technology, Shanghai 200093, China
- Institut Pasteur of Shanghai, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Junlei Yang
- Institute of Bismuth and Rhenium Science, School Materials and Chemistry, University of Shanghai for Science and Technology, Shanghai 200093, China
- Institut Pasteur of Shanghai, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Lihuan Yue
- CAS Key Laboratory of Molecular Virology & Immunology, Institutional Center for Shared Technologies and Facilities, Pathogen Discovery and Big Data Platform, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai 200031, China
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Bei Shen
- CAS Key Laboratory of Molecular Virology & Immunology, Institutional Center for Shared Technologies and Facilities, Pathogen Discovery and Big Data Platform, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai 200031, China
| | - Jing Wang
- Institut Pasteur of Shanghai, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
- CAS Key Laboratory of Molecular Virology & Immunology, Institutional Center for Shared Technologies and Facilities, Pathogen Discovery and Big Data Platform, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yuqing Miao
- Institute of Bismuth and Rhenium Science, School Materials and Chemistry, University of Shanghai for Science and Technology, Shanghai 200093, China
| | - Ruizhuo Ouyang
- Institute of Bismuth and Rhenium Science, School Materials and Chemistry, University of Shanghai for Science and Technology, Shanghai 200093, China
| | - Yihong Hu
- Institut Pasteur of Shanghai, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
- CAS Key Laboratory of Molecular Virology & Immunology, Institutional Center for Shared Technologies and Facilities, Pathogen Discovery and Big Data Platform, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai 200031, China
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3
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Asad N, Smith E, Shakya S, Stegman S, Timmons L. Sustainable Methodologies for Efficient Gel Electrophoresis and Streamlined Screening of Difficult Plasmids. Methods Protoc 2023; 6:mps6020025. [PMID: 36961045 PMCID: PMC10037626 DOI: 10.3390/mps6020025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 02/17/2023] [Accepted: 02/22/2023] [Indexed: 03/08/2023] Open
Abstract
We describe a workflow for efficient, environmentally attentive, and sustainable practices related to routine agarose gel electrophoresis. The methods reduce plastic waste and improve efficiency, especially for the exhaustive screening of difficult-to-obtain plasmids. Sustainability is increased when agarose is used ten times over by virtue of a thorough recycling regimen. The workflow optimizes workspaces and standardizes lab practices for handling potentially hazardous waste, minimizing environmental harm. Safety, efficiency, and sustainability improve laboratory productivity, help minimize environmental contamination, and increase cost-effectiveness.
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Affiliation(s)
- Nadeem Asad
- Department of Molecular Biosciences, The University of Kansas, 1200 Sunnyside Avenue, Lawrence, KS 66045, USA
- Department of Biochemistry and Molecular Medicine, 64 Medical Center Drive, University of West Virginia Health Science Center, Morgantown, WV 26506, USA
| | - Emily Smith
- Department of Molecular Biosciences, The University of Kansas, 1200 Sunnyside Avenue, Lawrence, KS 66045, USA
- Department of Neurobiology, Physiology & Behavior, University of California, Davis, CA 95618, USA
- Department of Psychiatry and Behavioral Sciences, University of California, Davis, CA 95618, USA
- Center for Neuroscience, University of California, Davis, CA 95618, USA
| | - Sudeep Shakya
- Department of Molecular Biosciences, The University of Kansas, 1200 Sunnyside Avenue, Lawrence, KS 66045, USA
| | - Sutton Stegman
- Department of Molecular Biosciences, The University of Kansas, 1200 Sunnyside Avenue, Lawrence, KS 66045, USA
| | - Lisa Timmons
- Department of Molecular Biosciences, The University of Kansas, 1200 Sunnyside Avenue, Lawrence, KS 66045, USA
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Garcia AGK, Steinbrenner AD. Bringing Plant Immunity to Light: A Genetically Encoded, Bioluminescent Reporter of Pattern-Triggered Immunity in Nicotiana benthamiana. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2023; 36:139-149. [PMID: 36583694 DOI: 10.1094/mpmi-07-22-0160-ta] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Plants rely on innate immune systems to defend against a wide variety of biotic attackers. Key components of innate immunity include cell-surface pattern-recognition receptors (PRRs), which recognize pest- and pathogen-associated molecular patterns (PAMPs). Unlike other classes of receptors that often have visible cell-death immune outputs upon activation, PRRs generally lack rapid methods for assessing function. Here, we describe a genetically encoded bioluminescent reporter of immune activation by heterologously expressed PRRs in the model organism Nicotiana benthamiana. We characterized N. benthamiana transcriptome changes in response to Agrobacterium tumefaciens and subsequent PAMP treatment to identify pattern-triggered immunity (PTI)-associated marker genes, which were then used to generate promoter-luciferase fusion fungal bioluminescence pathway (FBP) constructs. A reporter construct termed pFBP_2xNbLYS1::LUZ allows for robust detection of PTI activation by heterologously expressed PRRs. Consistent with known PTI signaling pathways, reporter activation by receptor-like protein (RLP) PRRs is dependent on the known adaptor of RLP PRRs, i.e., SOBIR1. The FBP reporter minimizes the amount of labor, reagents, and time needed to assay function of PRRs and displays robust sensitivity at biologically relevant PAMP concentrations, making it ideal for high throughput screens. The tools described in this paper will be powerful for investigations of PRR function and characterization of the structure-function of plant cell-surface receptors. [Formula: see text] The author(s) have dedicated the work to the public domain under the Creative Commons CC0 "No Rights Reserved" license by waiving all of his or her rights to the work worldwide under copyright law, including all related and neighboring rights, to the extent allowed by law, 2023.
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Affiliation(s)
- Anthony G K Garcia
- Department of Biology, University of Washington, Seattle, WA 98195, U.S.A
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5
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Oligo replication advantage driven by GC content and Gibbs free energy. Biotechnol Lett 2022; 44:1189-1199. [PMID: 36029395 DOI: 10.1007/s10529-022-03295-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 07/25/2022] [Indexed: 11/02/2022]
Abstract
Large scale DNA oligo pools are emerging as a novel material in a variety of advanced applications. However, GC content and length cause significant bias in amplification of oligos. We systematically explored the amplification of one oligo pool comprising of over ten thousand distinct strands with moderate GC content in the range of 35-65%. Uniqual amplification of oligos result to the increased Gini index of the oligo distribution while a few oligos greatly increased their proportion after 60 cycles of PCR. However, the significantly enriched oligos all have relatively high GC content. Further thermodynamic analysis demonstrated that a high value of both GC content and Gibbs free energy could improve the replication of specific oligos during biased amplification. Therefore, this double-G (GC content and Gibbs free energy) driven replication advantage can be used as a guiding principle for the sequence design for a variety of applications, particularly for data storage.
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6
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Ijaz F, Nakazato R, Setou M, Ikegami K. A pair of primers facing at the double-strand break site enables to detect NHEJ-mediated indel mutations at a 1-bp resolution. Sci Rep 2022; 12:11681. [PMID: 35804017 PMCID: PMC9270360 DOI: 10.1038/s41598-022-15776-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 06/29/2022] [Indexed: 11/11/2022] Open
Abstract
The introduction of small insertion/deletion (indel) mutations in the coding region of genes by the site-specific nucleases such as Cas9 allows researchers to obtain frameshift null mutants. Technically simple and costly reasonable genotyping methods are awaited to efficiently screen the frameshift null mutant candidates. Here, we developed a simple genotyping method called DST-PCR (Double-strand break Site-Targeted PCR) using “face-to-face” primers where the 3’ ends of forward and reverse primers face each other at the position between 3-bp and 4-bp upstream of the PAM sequence, which is generally the Cas9-mediated double-strand break site. Generated amplicons are directly subjected to TBE-High-Resolution PAGE, which contains a high concentration of bis-acrylamide, for mutant clones detection with 1-bp resolution. We present actual cases of screening of CRISPR/Cas9-engineered knockout (KO) cells for six genes, where we screen indels to obtain potential KO cell clones utilizing our approach. This method allowed us to detect 1-bp to 2-bp insertion and 1-bp to 4-bp deletion in one or both alleles of mutant cell clones. In addition, this technique also allowed the identification of heterozygous and homozygous biallelic functional KO candidates. Thus, DST-PCR is a simple and fast method to screen KO candidates generated by the CRISPR/Cas9 system before the final selection of clones with sequencing.
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Affiliation(s)
- Faryal Ijaz
- Department of Anatomy and Developmental Biology, Graduate School of Biomedical and Health Sciences, Hiroshima University, 1-2-3 Kasumi, Minami-Ku, Hiroshima, 734-8553, Japan
| | - Ryota Nakazato
- Department of Anatomy and Developmental Biology, Graduate School of Biomedical and Health Sciences, Hiroshima University, 1-2-3 Kasumi, Minami-Ku, Hiroshima, 734-8553, Japan
| | - Mitsutoshi Setou
- Department of Cellular and Molecular Anatomy and International Mass Imaging Center, Hamamatsu University School of Medicine, Hamamatsu, 431-3192, Japan
| | - Koji Ikegami
- Department of Anatomy and Developmental Biology, Graduate School of Biomedical and Health Sciences, Hiroshima University, 1-2-3 Kasumi, Minami-Ku, Hiroshima, 734-8553, Japan. .,Department of Cellular and Molecular Anatomy and International Mass Imaging Center, Hamamatsu University School of Medicine, Hamamatsu, 431-3192, Japan. .,JST, PRESTO, 4-1-8 Honcho, Kawaguchi, Saitama, 332-0012, Japan.
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7
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Chen MH, Abernathy E, Icenogle JP, Perelygina LM. Improved diagnostic and multiplex RT-qPCR for detecting rubella viral RNA. J Virol Methods 2022; 306:114555. [PMID: 35654258 DOI: 10.1016/j.jviromet.2022.114555] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 05/19/2022] [Accepted: 05/27/2022] [Indexed: 11/18/2022]
Abstract
An examination of the nucleic acid sequence alignment of 48 full-length rubella virus genomes revealed that the 5' terminus of the genome is more conserved than the commonly used detection windows for rubella virus RNA located in the E1 protein coding region, suggesting that the 5' terminus could be a target for improving detection of all rubella virus genotypes. Two candidate primer sets were tested and the window between nucleotides (nts) 98 and 251 was found to have the greatest analytical sensitivity for detection of different genotypes. The new method had a limit of detection of four copies of rubella RNA per reaction with high specificity. The average coefficient variation of Ct was 2.2%. Concordance between the new method and currently used method, based on testing 251 clinical specimens collected from a rubella outbreak, was 99.4%. The assay was further improved upon by the incorporation of detection of both rubella virus RNA and mRNA from a cellular reference gene in a multiplex format. The multiplex format did not reduce the sensitivity or the reproducibility of rubella RNA detection and, of 60 specimens tested, the concordance between the single target and multiplex assays was 85.0%. To assess the utility of the multiplex assay for molecular surveillance, 62 rubella IgM positive serum samples from a rubella outbreak were tested, and eleven tested positive using the multiplex method while none were positive using the method targeting E1. These results show that the assay based on the new detection window near the 5' terminus of the genome can improve the detection of rubella virus for the purpose of molecular surveillance and case confirmation, with the added benefit of improved efficiency due to multiplexing.
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Affiliation(s)
- Min-Hsin Chen
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA.
| | - Emily Abernathy
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA
| | - Joseph P Icenogle
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA
| | - Ludmila M Perelygina
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA
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Dhatterwal P, Mehrotra S, Mehrotra R. Primer Designing for Amplifying an AT-Rich Promoter from Arabidopsis thaliana. Methods Mol Biol 2022; 2392:115-123. [PMID: 34773619 DOI: 10.1007/978-1-0716-1799-1_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The aim of the present study is to optimize the PCR conditions required to amplify the promoter sequence of an amino acid transporter having an AT-rich base composition with a high number of tandem repeats. The present study also covers the key parameters that need to be kept in mind while designing primers. Results show that successful can be achieved by performing a 2-step PCR reaction at a lower extension temperature of 65 ̊C for an increased extension period of 1.5 min/kb, with MgCl2 concentration ranging from 2.5 to 3.0mM. The results also suggest that the DNA concentration of around 25-30 ng/µl was essential to achieve this amplification.
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Affiliation(s)
- Pinky Dhatterwal
- Department of Biological Sciences, Birla Institute of Technology & Science Pilani, Sancoale, Goa, India
| | - Sandhya Mehrotra
- Department of Biological Sciences, Birla Institute of Technology & Science Pilani, Sancoale, Goa, India
| | - Rajesh Mehrotra
- Department of Biological Sciences, Birla Institute of Technology & Science Pilani, Sancoale, Goa, India.
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9
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Nucleotide amplification and sequencing of the GC-rich region between matrix and fusion protein genes of peste des petits ruminants virus. J Virol Methods 2021; 300:114390. [PMID: 34848280 DOI: 10.1016/j.jviromet.2021.114390] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2021] [Revised: 06/08/2021] [Accepted: 11/26/2021] [Indexed: 01/05/2023]
Abstract
Peste des petits ruminants virus (PPRV) causes a highly devastating disease of sheep and goats, that threatens the conservation of small wild ruminants. The development of PPRV vaccines, diagnostics and therapeutics, greatly depends on in-depth genomic data. Yet, high guanine-cytosine (GC) content between matrix (M) and fusion (F) genes of PPRV poses difficulty for both primer design and nucleotide amplification. In turn, this has led into absence or low nucleotide sequence coverage in this region. This poses a risk of missing important part of the genome that could help to infer viral evolution. Here, an overlapping long-read primer-based amplification strategy was developed to amplify the GC-rich fragments between M-F gene junction using nexus gradient polymerase chain reaction (PCR). The resulting amplicons were sequenced by dideoxynucleotide cycle sequencing and compared with other PPRV nucleotide sequences available at GenBank. Our findings indicate clear PCR amplification products with expected size of the GC-rich fragments on agarose gel electrophoresis. The sequencing results of these fragments indicate 99.5 % nucleotide identity with PPRV strain KY628761. An extremely difficult PCR target of 67.4 % GC contents was successfully amplified and sequenced using this long-read primer approach. The long-read primer set may be used in tiling multiplex PCR for complete genome sequencing of PPRV.
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10
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Eleizalde MC, Gómez-Piñeres E, Ramírez-Iglesias JR, Mendoza M. Evaluation of five primer sets for molecular detection of Trypanosoma vivax by polymerase chain reaction (PCR) and their implementation for diagnosis in naturally infected ruminants from Venezuela. Vet Parasitol Reg Stud Reports 2021; 25:100594. [PMID: 34474787 DOI: 10.1016/j.vprsr.2021.100594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2020] [Revised: 03/28/2021] [Accepted: 05/23/2021] [Indexed: 11/16/2022]
Abstract
Trypanosoma vivax is a protozoan parasite that causes trypanosomosis in ruminants and is widely distributed in tropical areas in the world. The control of this disease depends on the sensitivity and specificity of the diagnostic tests implemented for naturally infected samples, where parasitaemias are usually low. This study aimed to evaluate the analytical sensitivity and specificity of several primers for T. vivax detection in experimental infections and their implementation for the diagnosis of trypanosomosis in naturally infected bovine and ovine samples. Using a T. vivax Venezuelan isolate, five sets of primers were evaluated: TviSL1/2, ITS1CF/BR, TVMF/R, ILO1264/1265, TVWA/B. Additionally, we tested the PCR protocols using different DNA quantities. The best set of primers (ILO1264/1265) was used to detect T. vivax DNA from whole blood and buffy coat samples of 12 sheep (ovine) and 45 cattle (bovine) of small farms from Venezuela, and compared to the micro-haematocrite centrifugation technique (MHCT). The highest sensitivity was 0.0001 ng for ILO1264/1265 and TVWA/B primers. Using 100 ng of DNA extracted from the buffy coat and the ILO1264/1265 primers for trypanosomosis diagnosis from naturally infected samples, yielded 66.7% (8/12) and 35.7% (16/45) positives in ovine and bovine respectively. The percentage of positives samples increased to 83.3% (10/12) and 64.4% (29/45), with 300 ng in the assays. Contrary, using 300 ng of DNA extracted from the whole blood yielded only 50% (6/12) and 28.9% (13/45) of positives samples for T. vivax respectively. MHCT only detected the parasite in bovine samples with 17.8% (8/45) of positives. Based on our results, we recommend the use of the ILO1264/1265 primers and 300 ng of DNA extracted from the buffy coat for epidemiological studies of naturally infected animals. Moreover, detection of the parasite in ovine herds highlights a possible role of this host in the epidemiology of trypanosomosis in Venezuela.
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Affiliation(s)
- M C Eleizalde
- Centro de Estudios Biomédicos y Veterinarios (CEBIV), Instituto de Estudios Científicos y Tecnológicos (IDECYT), Universidad Nacional Experimental Simón Rodríguez, Apartado Postal 47925, Caracas, Venezuela
| | - E Gómez-Piñeres
- Núcleo Monagas, Escuela de Zootecnia, Departamento de Biología y Sanidad Animal, Universidad de Oriente, Maturín, Venezuela
| | - J R Ramírez-Iglesias
- Group for Neglected-Emerging Diseases, Eco-Epidemiology and Biodiversity, Health Sciences Faculty, Universidad Internacional SEK, Quito, Ecuador
| | - M Mendoza
- Centro de Estudios Biomédicos y Veterinarios (CEBIV), Instituto de Estudios Científicos y Tecnológicos (IDECYT), Universidad Nacional Experimental Simón Rodríguez, Apartado Postal 47925, Caracas, Venezuela.
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11
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Emrich-Mills TZ, Yates G, Barrett J, Girr P, Grouneva I, Lau CS, Walker CE, Kwok TK, Davey JW, Johnson MP, Mackinder LCM. A recombineering pipeline to clone large and complex genes in Chlamydomonas. THE PLANT CELL 2021; 33:1161-1181. [PMID: 33723601 PMCID: PMC8633747 DOI: 10.1093/plcell/koab024] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 01/18/2021] [Indexed: 05/10/2023]
Abstract
The ability to clone genes has greatly advanced cell and molecular biology research, enabling researchers to generate fluorescent protein fusions for localization and confirm genetic causation by mutant complementation. Most gene cloning is polymerase chain reaction (PCR)�or DNA synthesis-dependent, which can become costly and technically challenging as genes increase in size, particularly if they contain complex regions. This has been a long-standing challenge for the Chlamydomonas reinhardtii research community, as this alga has a high percentage of genes containing complex sequence structures. Here we overcame these challenges by developing a recombineering pipeline for the rapid parallel cloning of genes from a Chlamydomonas bacterial artificial chromosome collection. To generate fluorescent protein fusions for localization, we applied the pipeline at both batch and high-throughput scales to 203 genes related to the Chlamydomonas CO2 concentrating mechanism (CCM), with an overall cloning success rate of 77%. Cloning success was independent of gene size and complexity, with cloned genes as large as 23 kb. Localization of a subset of CCM targets confirmed previous mass spectrometry data, identified new pyrenoid components, and enabled complementation of mutants. We provide vectors and detailed protocols to facilitate easy adoption of this technology, which we envision will open up new possibilities in algal and plant research.
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Affiliation(s)
- Tom Z Emrich-Mills
- Department of Biology, University of York, York YO10 5DD, UK
- Department Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, UK
| | - Gary Yates
- Department of Biology, University of York, York YO10 5DD, UK
| | - James Barrett
- Department of Biology, University of York, York YO10 5DD, UK
| | - Philipp Girr
- Department of Biology, University of York, York YO10 5DD, UK
| | - Irina Grouneva
- Department of Biology, University of York, York YO10 5DD, UK
| | - Chun Sing Lau
- Department of Biology, University of York, York YO10 5DD, UK
| | | | - Tsz Kam Kwok
- Department of Biology, University of York, York YO10 5DD, UK
| | - John W Davey
- Department of Biology, University of York, York YO10 5DD, UK
| | - Matthew P Johnson
- Department Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, UK
| | - Luke C M Mackinder
- Department of Biology, University of York, York YO10 5DD, UK
- Author for correspondence: (L.C.M.M.)
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12
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Ahmed S, Hossain Z, Uddin M, Taherzadeh G, Sharma A, Shatabda S, Dehzangi A. Accurate prediction of RNA 5-hydroxymethylcytosine modification by utilizing novel position-specific gapped k-mer descriptors. Comput Struct Biotechnol J 2020; 18:3528-3538. [PMID: 33304452 PMCID: PMC7701324 DOI: 10.1016/j.csbj.2020.10.032] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 10/30/2020] [Accepted: 10/30/2020] [Indexed: 12/13/2022] Open
Abstract
RNA modification is an essential step towards generation of new RNA structures. Such modification is potentially able to modify RNA function or its stability. Among different modifications, 5-Hydroxymethylcytosine (5hmC) modification of RNA exhibit significant potential for a series of biological processes. Understanding the distribution of 5hmC in RNA is essential to determine its biological functionality. Although conventional sequencing techniques allow broad identification of 5hmC, they are both time-consuming and resource-intensive. In this study, we propose a new computational tool called iRNA5hmC-PS to tackle this problem. To build iRNA5hmC-PS we extract a set of novel sequence-based features called Position-Specific Gapped k-mer (PSG k-mer) to obtain maximum sequential information. Our feature analysis shows that our proposed PSG k-mer features contain vital information for the identification of 5hmC sites. We also use a group-wise feature importance calculation strategy to select a small subset of features containing maximum discriminative information. Our experimental results demonstrate that iRNA5hmC-PS is able to enhance the prediction performance, dramatically. iRNA5hmC-PS achieves 78.3% prediction performance, which is 12.8% better than those reported in the previous studies. iRNA5hmC-PS is publicly available as an online tool at http://103.109.52.8:81/iRNA5hmC-PS. Its benchmark dataset, source codes, and documentation are available at https://github.com/zahid6454/iRNA5hmC-PS.
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Affiliation(s)
- Sajid Ahmed
- Department of Computer Science and Engineering, United International University, Dhaka, Bangladesh
| | - Zahid Hossain
- Department of Computer Science and Engineering, United International University, Dhaka, Bangladesh
| | - Mahtab Uddin
- Department of Natural Science, United International University, Dhaka, Bangladesh
| | - Ghazaleh Taherzadeh
- Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, MD 20742, USA
| | - Alok Sharma
- Institute for Integrated and Intelligent Systems, Griffith University, Brisbane, QLD 4111, Australia.,Department of Medical Science Mathematics, Tokyo Medical and Dental University (TMDU), Tokyo, Japan.,Laboratory for Medical Science Mathematics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.,School of Engineering and Physics, University of the South Pacific, Suva, Fiji
| | - Swakkhar Shatabda
- Department of Computer Science and Engineering, United International University, Dhaka, Bangladesh
| | - Abdollah Dehzangi
- Department of Computer Science, Rutgers University, Camden, NJ 08102, USA.,Center for Computational and Integrative Biology, Rutgers University, Camden, NJ 08102, USA
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13
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Liu Z, Sun J, Zhao G, Xiong S, Ma Y, Zheng M. Transient stem-loop structure of nucleic acid template may interfere with polymerase chain reaction through endonuclease activity of Taq DNA polymerase. Gene 2020; 764:145095. [PMID: 32866587 DOI: 10.1016/j.gene.2020.145095] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Revised: 08/18/2020] [Accepted: 08/24/2020] [Indexed: 12/14/2022]
Abstract
As a standard molecular biology technique, PCR uses DNA polymerase to detect, amplify and manipulate DNA targets. Due to its effect of exponential amplification, PCR can achieve high sensitivity required for detecting targets of low abundance. Therefore, it has become the method of choice for the majority of nucleic acid-based tests. In PCR reactions, DNA templates are first unwound into single strands, followed by a quick temperature drop when transient intramolecular secondary structures may form first within the single-stranded templates due to reaction kinetics. In this study, we showed that the adverse effects of stem-loop structures on PCR performance were directly correlated with their thermal stability. Moreover, fractions of intermediate PCR products of templates with stable stem-loop structures were significantly shorter than those without. It was further demonstrated that when encountering the duplex region of such a structure during the PCR extension step, the endonuclease activity of Taq DNA polymerase mediated by its 5'-3' exonuclease activity could digest template strand, resulting in stem-loop structure unwinding and subsequent completion of replication to produce truncated products. This work thus provided some new mechanistic insights into the complex nature of PCR assays, a frequently encountered but neglected aspect of this widely used technique.
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Affiliation(s)
- Zhaocheng Liu
- University of Science and Technology of China, Hefei, Anhui 230027, China; Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, Jiangsu 215163, China
| | - Jinli Sun
- University of Science and Technology of China, Hefei, Anhui 230027, China; Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, Jiangsu 215163, China
| | - Guodong Zhao
- Zhejiang University Kunshan Biotechnology Laboratory, Zhejiang University Kunshan Innovation Institute, Kunshan, Jiangsu 215300, China; Suzhou VersaBio Technologies Co. Ltd., Kunshan, Jiangsu 215300, China; State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, Jiangsu 210009, China
| | - Shangmin Xiong
- Zhejiang University Kunshan Biotechnology Laboratory, Zhejiang University Kunshan Innovation Institute, Kunshan, Jiangsu 215300, China; Suzhou VersaBio Technologies Co. Ltd., Kunshan, Jiangsu 215300, China.
| | - Yong Ma
- University of Science and Technology of China, Hefei, Anhui 230027, China; Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, Jiangsu 215163, China.
| | - Minxue Zheng
- University of Science and Technology of China, Hefei, Anhui 230027, China; Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, Jiangsu 215163, China.
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14
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Mishra A, Dhali A, Reddy IJ, Kolte AP. Sexing of pre-implantation ovine embryos through polymerase chain reaction-based amplification of GAPDH, SRY and AMEL genes. Reprod Domest Anim 2020; 55:885-892. [PMID: 32379910 DOI: 10.1111/rda.13699] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Accepted: 04/24/2020] [Indexed: 11/27/2022]
Abstract
The ability to identify the sex of embryo and control of sex ratio has a great commercial importance to livestock industry. Prediction of embryonic sex could be useful in the management decisions of sex selection in breeding programs. Several methods have been attempted to determine the sex but the polymerase chain reaction (PCR)-based sexing method is generally favoured, as it is cost effective, simple and reliable. The aim of the present study was to identify sex of sheep embryos produced in vitro through amplification of glyceraldehyde 3-phosphate dehydrogenase (GAPDH), sex-determining region Y (SRY) and amelogenin genes present in genomic DNA (gDNA) of embryos through PCR. To avoid false interpretation of the result by no amplification of SRY in female embryos, a duplex PCR was approached to amplify combinedly SRY and GAPDH genes. Sex-specific blood was used in PCR as positive control. In vitro sheep embryos were produced as per standardized protocol of laboratory. Sexing of sex-specific blood and in vitro produced embryos were approached though PCR to amplify the respective genes using gDNA present in the sample without its traditional isolation. The accuracy of sex prediction for embryos was 100% by this procedure.
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Affiliation(s)
- Ashish Mishra
- ICAR-National Institute of Animal Nutrition and Physiology, Bangalore, India
| | - Arindam Dhali
- ICAR-National Institute of Animal Nutrition and Physiology, Bangalore, India
| | - Ippala J Reddy
- ICAR-National Institute of Animal Nutrition and Physiology, Bangalore, India
| | - Atul P Kolte
- ICAR-National Institute of Animal Nutrition and Physiology, Bangalore, India
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15
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Tsai TT, Chen CA, Yi-Ju Ho N, Yang S, Chen CF. Fluorescent Double-Stranded DNA-Templated Copper Nanoprobes for Rapid Diagnosis of Tuberculosis. ACS Sens 2019; 4:2885-2892. [PMID: 31576745 DOI: 10.1021/acssensors.9b01163] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
In this work, we investigate highly sensitive fluorescent Cu nanoparticles for use as rapid and specific nucleic acid amplification nanoprobes (NPs) for the diagnosis of tuberculosis. After applying polymerase chain reaction (PCR) to a tuberculosis (TB) sample, we demonstrate that the presence of the targeted IS6110 DNA sequence of TB can be easily and directly detected through the in situ formation of DNA-templated fluorescent Cu NPs and subsequently quantified using only a smartphone. Compared to traditional DNA analysis, this sensing platform does not require purification steps and eliminates the need for electrophoresis to confirm the PCR results. After optimization, this dsDNA-Cu NP-PCR method has the ability to analyze clinical TB nucleic acid samples at a detection limit of 5 fg/μL, and the fluorescent signal can be distinguished in only ∼3 min after the DNA has been amplified. Moreover, with the combination of smartphone-assisted imaging analysis, we can further reduce the instrument size/cost and enhance the portability. In this manner, we are able to eliminate the need for a fluorescent spectrophotometer to measure the clinical sample. These results demonstrate this platform's practical applicability, combining a smartphone and on-site analysis while retaining the detection performance, making it suitable for clinical DNA applications in resource-limited regions of the world.
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Affiliation(s)
- Tsung-Ting Tsai
- Department of Orthopaedic Surgery, Bone and Joint Research Center, Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Taoyuan 333, Taiwan
| | - Chung-An Chen
- Institute of Applied Mechanics, National Taiwan University, Taipei 106, Taiwan
| | - Natalie Yi-Ju Ho
- Department of Orthopaedic Surgery, Bone and Joint Research Center, Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Taoyuan 333, Taiwan
| | - Shuan Yang
- Department of Laboratory Medicine, Chang Gung Memorial Hospital, Taoyuan 333, Taiwan
| | - Chien-Fu Chen
- Institute of Applied Mechanics, National Taiwan University, Taipei 106, Taiwan
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16
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Green MR, Sambrook J. Polymerase Chain Reaction (PCR) Amplification of GC-Rich Templates. Cold Spring Harb Protoc 2019; 2019:2019/2/pdb.prot095141. [PMID: 30710022 DOI: 10.1101/pdb.prot095141] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The efficiency of polymerase chain reaction (PCR) amplification is influenced by the nucleotide composition and sequence of the template DNA. Problematic templates include those with long homopolymeric runs, inverted repeats, or GC-rich tracts-such as those containing >60% G + C residues-that are found in the regulatory regions of many mammalian genes. Localized regions of templates rich in GC residues tend to fold into complex secondary structures that might not melt during the annealing phase of the PCR cycle. Also, the primers used to amplify GC-rich regions often have a high capacity to form self- and cross-dimers and a strong tendency to fold into stem-loop structures that can impede the progress of the DNA polymerase along the template molecule. Predictably, amplification of full-length template DNA is inefficient, and the products of the reaction contain a high proportion of shorter molecules that result from blockage of the DNA polymerase. Altering the design of the primers and using a combination of hot start and touchdown PCR can sometimes improve the efficiency of amplification. More often, a multipronged approach is required, such as the use of enhancers in the amplification reaction, adjustment of the cycling protocol, and, if necessary, designing new sets of primers. This protocol uses a mixture of four additives-betaine, dithiothreitol (DTT), dimethyl sulfoxide (DMSO), and bovine serum albumin (BSA)-for use with Taq DNA polymerase.
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17
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Jaffarali M, Hall A. Transcriptional regulation of protein S gene. HAMDAN MEDICAL JOURNAL 2019. [DOI: 10.4103/hmj.hmj_49_18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
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18
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Li A, Acevedo-Rocha CG, Reetz MT. Boosting the efficiency of site-saturation mutagenesis for a difficult-to-randomize gene by a two-step PCR strategy. Appl Microbiol Biotechnol 2018; 102:6095-6103. [PMID: 29785500 PMCID: PMC6013526 DOI: 10.1007/s00253-018-9041-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Revised: 04/13/2018] [Accepted: 04/19/2018] [Indexed: 12/31/2022]
Abstract
Site-saturation mutagenesis (SSM) has been used in directed evolution of proteins for a long time. As a special form of saturation mutagenesis, it involves individual randomization at a given residue with formation of all 19 amino acids. To date, the most efficient embodiment of SSM is a one-step PCR-based approach using NNK codon degeneracy. However, in the case of difficult-to-randomize genes, SSM may not deliver all of the expected 19 mutants, which compels the user to invest further efforts by applying site-directed mutagenesis for the construction of the missing mutants. To solve this problem, we developed a two-step PCR-based technique in which a mutagenic primer and a non-mutagenic (silent) primer are used to generate a short DNA fragment, which is recovered and then employed as a megaprimer to amplify the whole plasmid. The present two-step and older one-step (partially overlapped primer approach) procedures were compared by utilizing cytochrome P450-BM3, which is a "difficult-to-randomize" gene. The results document the distinct superiority of the new method by checking the library quality on DNA level based on massive sequence data, but also at amino acid level. Various future applications in biotechnology can be expected, including the utilization when constructing mutability landscapes, which provide semi-rational information for identifying hot spots for protein engineering and directed evolution.
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Affiliation(s)
- Aitao Li
- Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Hubei Key Laboratory of Industrial Biotechnology, College of Life Sciences, Hubei University, Wuhan, 430062, China.,Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470, Muelheim, Germany.,Department of Chemistry, Philipps-Universität, Hans-Meerwein-Strasse 4, 35032, Marburg, Germany
| | | | - Manfred T Reetz
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470, Muelheim, Germany. .,Department of Chemistry, Philipps-Universität, Hans-Meerwein-Strasse 4, 35032, Marburg, Germany.
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19
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Ratnayake D, Newman M, Lardelli M. Degenerate codon mixing for PCR-based manipulation of highly repetitive sequences. BMC Res Notes 2018; 11:202. [PMID: 29587822 PMCID: PMC5870680 DOI: 10.1186/s13104-018-3298-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Accepted: 03/20/2018] [Indexed: 11/24/2022] Open
Abstract
Objective Repeat expansion of polyglutamine tracks leads to a group of inherited human neurodegenerative disorders. Studying such repetitive sequences is required to gain insight into the pathophysiology of these diseases. PCR-based manipulation of repetitive sequences, however, is challenging due to the absence of unique primer binding sites or the generation of non-specific products. Results We have utilised the degeneracy of the genetic code to generate a polyglutamine sequence with low repeat similarity. This strategy allowed us to use conventional PCR to generate multiple constructs with approximately defined numbers of glutamine repeats. We then used these constructs to measure the in vivo variation in autophagic degradation activity related to the different numbers of glutamine repeats, providing an example of their applicability to study repeat expansion diseases. Our simple and easily generalised method of generating low repetition DNA sequences coding for uniform stretches of amino acid residues provides a strategy for generating particular lengths of polyglutamine tracts using standard PCR and cloning protocols. Electronic supplementary material The online version of this article (10.1186/s13104-018-3298-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Dhanushika Ratnayake
- School of Biological Sciences, Alzheimer's Disease Genetics Laboratory, University of Adelaide, North Terrace, Adelaide, SA, 5005, Australia.,Australian Regenerative Medicine Institute, Monash University, Wellington Road, Clayton, 3800, Australia
| | - Morgan Newman
- School of Biological Sciences, Alzheimer's Disease Genetics Laboratory, University of Adelaide, North Terrace, Adelaide, SA, 5005, Australia
| | - Michael Lardelli
- School of Biological Sciences, Alzheimer's Disease Genetics Laboratory, University of Adelaide, North Terrace, Adelaide, SA, 5005, Australia.
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20
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Liu Y, Erséus C. New specific primers for amplification of the Internal Transcribed Spacer region in Clitellata (Annelida). Ecol Evol 2017; 7:10421-10439. [PMID: 29238565 PMCID: PMC5723599 DOI: 10.1002/ece3.3212] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Revised: 06/05/2017] [Accepted: 06/06/2017] [Indexed: 11/11/2022] Open
Abstract
Nuclear molecular evidence, for example, the rapidly evolving Internal Transcribed Spacer region (ITS), integrated with maternally inherited (mitochondrial) COI barcodes, has provided new insights into the diversity of clitellate annelids. PCR amplification and sequencing of ITS, however, are often hampered by poor specificity of primers used. Therefore, new clitellate‐specific primers for amplifying the whole ITS region (ITS: 29F/1084R) and a part of it (ITS2: 606F/1082R) were developed on the basis of a collection of previously published ITS sequences with flanking rDNA coding regions. The specificity of these and other ITS primers used for clitellates were then tested in silico by evaluating their mismatches with all assembled and annotated sequences (STD, version r127) from EMBL, and the new primers were also tested in vitro for a taxonomically broad sample of clitellate species (71 specimens representing 11 families). The in silico analyses showed that the newly designed primers have a better performance than the universal ones when amplifying clitellate ITS sequences. In vitro PCR and sequencing using the new primers were successful, in particular, for the 606F/1082R pair, which worked well for 65 of the 71 specimens. Thus, using this pair for amplifying the ITS2 will facilitate further molecular systematic investigation of various clitellates. The other pair (29F/1084R), will be a useful complement to existing ITS primers, when amplifying ITS as a whole.
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Affiliation(s)
- Yingkui Liu
- Department of Biological and Environmental Sciences University of Gothenburg Göteborg Sweden
| | - Christer Erséus
- Department of Biological and Environmental Sciences University of Gothenburg Göteborg Sweden
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21
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Dhatterwal P, Mehrotra S, Mehrotra R. Optimization of PCR conditions for amplifying an AT-rich amino acid transporter promoter sequence with high number of tandem repeats from Arabidopsis thaliana. BMC Res Notes 2017; 10:638. [PMID: 29183338 PMCID: PMC5706289 DOI: 10.1186/s13104-017-2982-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Accepted: 11/22/2017] [Indexed: 11/10/2022] Open
Abstract
OBJECTIVE The aim of the present study is to optimize the PCR conditions required to amplify the promoter sequence of an amino acid transporter having an AT-rich base composition with a high number of tandem repeats. RESULT Results show that successful amplification can be achieved by performing a 2-step PCR at a lower extension temperature of 65 °C for an increased extension period of 1.5 min/kb, with MgCl2 concentration ranging from 2.5 to 3.0 mM. The results also suggest that the DNA concentration of about 25-30 ng/µl was essential to achieve this amplification.
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Affiliation(s)
- Pinky Dhatterwal
- Department of Biological Sciences, Birla Institute of Technology & Sciences, Pilani, Rajasthan, 333031, India
| | - Sandhya Mehrotra
- Department of Biological Sciences, Birla Institute of Technology & Sciences, Pilani, Rajasthan, 333031, India.
| | - Rajesh Mehrotra
- Department of Biological Sciences, Birla Institute of Technology & Sciences, Pilani, Rajasthan, 333031, India.
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22
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Yang Z, Sun G. High-frequency, low-coverage "false positives" mutations may be true in GS Junior sequencing studies. Sci Rep 2017; 7:13751. [PMID: 29062110 PMCID: PMC5653793 DOI: 10.1038/s41598-017-13116-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Accepted: 09/19/2017] [Indexed: 12/29/2022] Open
Abstract
The GS Junior sequencer provides simplified procedures for library preparation and data processing. Errors in pyrosequencing generate some biases during library construction and emulsion PCR amplification. False-positive mutations are identified by related characteristics described in the manufacturer’s manual, and some detected mutations may have ‘borderline’ characteristics when they are detected in few reads or at low frequency. Among these mutations, however, some may be true positives. This study aimed to improve the accuracy of identifying true positives among mutations with borderline false-positive characteristics detected with GS Junior sequencing. Mutations with the borderline features were tested for validity with Sanger sequencing. We examined 10 mutations detected in coverages <20-fold at frequencies >30% (group A) and 16 mutations detected in coverages >20-fold at frequencies < 30% (group B). In group A, two mutations were not confirmed, and two mutations with 100% frequency were confirmed as heterozygous alleles. No mutation in group B was confirmed. The two groups had significantly different false-positive prevalences (p = 0.001). These results suggest that mutations detected at frequencies less than 30% can be confidently identified as false-positives but that mutations detected at frequencies over 30%, despite coverages less than 20-fold, should be verified with Sanger sequencing.
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Affiliation(s)
- Zhiliang Yang
- Department of Pediatrics, the First Hospital of China Medical University, Shenyang, 110001, China.
| | - Guilian Sun
- Department of Pediatrics, the First Hospital of China Medical University, Shenyang, 110001, China
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23
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Jurišić V, Obradović J, Tošić N, Pavlović S, Kulić M, Djordjević N. Effects of DMSO, glycerol, betaine and their combinations in detecting single nucleotide polymorphisms of epidermal growth factor receptor (EGFR) gene promoter sequence in non-small-cell lung cancer (NSCLC) patients. J Pharm Biomed Anal 2016; 128:275-279. [DOI: 10.1016/j.jpba.2016.05.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Revised: 05/02/2016] [Accepted: 05/05/2016] [Indexed: 10/21/2022]
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24
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Guido N, Starostina E, Leake D, Saaem I. Improved PCR Amplification of Broad Spectrum GC DNA Templates. PLoS One 2016; 11:e0156478. [PMID: 27271574 PMCID: PMC4896431 DOI: 10.1371/journal.pone.0156478] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Accepted: 05/16/2016] [Indexed: 11/28/2022] Open
Abstract
Many applications in molecular biology can benefit from improved PCR amplification of DNA segments containing a wide range of GC content. Conventional PCR amplification of DNA sequences with regions of GC less than 30%, or higher than 70%, is complex due to secondary structures that block the DNA polymerase as well as mispriming and mis-annealing of the DNA. This complexity will often generate incomplete or nonspecific products that hamper downstream applications. In this study, we address multiplexed PCR amplification of DNA segments containing a wide range of GC content. In order to mitigate amplification complications due to high or low GC regions, we tested a combination of different PCR cycling conditions and chemical additives. To assess the fate of specific oligonucleotide (oligo) species with varying GC content in a multiplexed PCR, we developed a novel method of sequence analysis. Here we show that subcycling during the amplification process significantly improved amplification of short template pools (~200 bp), particularly when the template contained a low percent of GC. Furthermore, the combination of subcycling and 7-deaza-dGTP achieved efficient amplification of short templates ranging from 10-90% GC composition. Moreover, we found that 7-deaza-dGTP improved the amplification of longer products (~1000 bp). These methods provide an updated approach for PCR amplification of DNA segments containing a broad range of GC content.
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Affiliation(s)
- Nicholas Guido
- Research & Development, Gen9 Inc, Cambridge, Massachusetts, United States of America
| | - Elena Starostina
- Research & Development, Gen9 Inc, Cambridge, Massachusetts, United States of America
| | - Devin Leake
- Research & Development, Gen9 Inc, Cambridge, Massachusetts, United States of America
| | - Ishtiaq Saaem
- Research & Development, Gen9 Inc, Cambridge, Massachusetts, United States of America
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25
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Mayr R, Haider M, Thünauer R, Haselgrübler T, Schütz GJ, Sonnleitner A, Hesse J. A microfluidic platform for transcription- and amplification-free detection of zepto-mole amounts of nucleic acid molecules. Biosens Bioelectron 2016; 78:1-6. [DOI: 10.1016/j.bios.2015.11.013] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Revised: 11/04/2015] [Accepted: 11/05/2015] [Indexed: 11/15/2022]
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26
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Fikru R, Matetovici I, Rogé S, Merga B, Goddeeris BM, Büscher P, Van Reet N. Ribosomal DNA analysis of tsetse and non-tsetse transmitted Ethiopian Trypanosoma vivax strains in view of improved molecular diagnosis. Vet Parasitol 2016; 220:15-22. [DOI: 10.1016/j.vetpar.2016.02.013] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2015] [Revised: 02/09/2016] [Accepted: 02/11/2016] [Indexed: 11/16/2022]
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27
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Seroussi E, Cinnamon Y, Yosefi S, Genin O, Smith JG, Rafati N, Bornelöv S, Andersson L, Friedman-Einat M. Identification of the Long-Sought Leptin in Chicken and Duck: Expression Pattern of the Highly GC-Rich Avian leptin Fits an Autocrine/Paracrine Rather Than Endocrine Function. Endocrinology 2016; 157:737-51. [PMID: 26587783 DOI: 10.1210/en.2015-1634] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
More than 20 years after characterization of the key regulator of mammalian energy balance, leptin, we identified the leptin (LEP) genes of chicken (Gallus gallus) and duck (Anas platyrhynchos). The extreme guanine-cytosine content (∼70%), the location in a genomic region with low-complexity repetitive and palindromic sequence elements, the relatively low sequence conservation, and low level of expression have hampered the identification of these genes until now. In vitro-expressed chicken and duck leptins specifically activated signaling through the chicken leptin receptor in cell culture. In situ hybridization demonstrated expression of LEP mRNA in granular and Purkinje cells of the cerebellum, anterior pituitary, and in embryonic limb buds, somites, and branchial arches, suggesting roles in adult brain control of energy balance and during embryonic development. The expression patterns of LEP and the leptin receptor (LEPR) were explored in chicken, duck, and quail (Coturnix japonica) using RNA-sequencing experiments available in the Short Read Archive and by quantitative RT-PCR. In adipose tissue, LEP and LEPR were scarcely transcribed, and the expression level was not correlated to adiposity. Our identification of the leptin genes in chicken and duck genomes resolves a long lasting controversy regarding the existence of leptin genes in these species. This identification was confirmed by sequence and structural similarity, conserved exon-intron boundaries, detection in numerous genomic, and transcriptomic datasets and characterization by PCR, quantitative RT-PCR, in situ hybridization, and bioassays. Our results point to an autocrine/paracrine mode of action for bird leptin instead of being a circulating hormone as in mammals.
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Affiliation(s)
- Eyal Seroussi
- Agricultural Research Organization (E.S., Y.C., S.Y., O.G., J.G.-S., M.F.-E.), Volcani Center, 50250 Bet-Dagan, Israel; Department of Medical Biochemistry and Microbiology (N.R., S.B., L.A.), Uppsala University, SE-75123 Uppsala, Sweden; Department of Animal Breeding and Genetics (L.A.), Swedish University of Agricultural Sciences, SE-75007 Uppsala, Sweden; and Department of Veterinary Integrative Biosciences (L.A.), College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas 77843-4458
| | - Yuval Cinnamon
- Agricultural Research Organization (E.S., Y.C., S.Y., O.G., J.G.-S., M.F.-E.), Volcani Center, 50250 Bet-Dagan, Israel; Department of Medical Biochemistry and Microbiology (N.R., S.B., L.A.), Uppsala University, SE-75123 Uppsala, Sweden; Department of Animal Breeding and Genetics (L.A.), Swedish University of Agricultural Sciences, SE-75007 Uppsala, Sweden; and Department of Veterinary Integrative Biosciences (L.A.), College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas 77843-4458
| | - Sara Yosefi
- Agricultural Research Organization (E.S., Y.C., S.Y., O.G., J.G.-S., M.F.-E.), Volcani Center, 50250 Bet-Dagan, Israel; Department of Medical Biochemistry and Microbiology (N.R., S.B., L.A.), Uppsala University, SE-75123 Uppsala, Sweden; Department of Animal Breeding and Genetics (L.A.), Swedish University of Agricultural Sciences, SE-75007 Uppsala, Sweden; and Department of Veterinary Integrative Biosciences (L.A.), College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas 77843-4458
| | - Olga Genin
- Agricultural Research Organization (E.S., Y.C., S.Y., O.G., J.G.-S., M.F.-E.), Volcani Center, 50250 Bet-Dagan, Israel; Department of Medical Biochemistry and Microbiology (N.R., S.B., L.A.), Uppsala University, SE-75123 Uppsala, Sweden; Department of Animal Breeding and Genetics (L.A.), Swedish University of Agricultural Sciences, SE-75007 Uppsala, Sweden; and Department of Veterinary Integrative Biosciences (L.A.), College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas 77843-4458
| | - Julia Gage Smith
- Agricultural Research Organization (E.S., Y.C., S.Y., O.G., J.G.-S., M.F.-E.), Volcani Center, 50250 Bet-Dagan, Israel; Department of Medical Biochemistry and Microbiology (N.R., S.B., L.A.), Uppsala University, SE-75123 Uppsala, Sweden; Department of Animal Breeding and Genetics (L.A.), Swedish University of Agricultural Sciences, SE-75007 Uppsala, Sweden; and Department of Veterinary Integrative Biosciences (L.A.), College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas 77843-4458
| | - Nima Rafati
- Agricultural Research Organization (E.S., Y.C., S.Y., O.G., J.G.-S., M.F.-E.), Volcani Center, 50250 Bet-Dagan, Israel; Department of Medical Biochemistry and Microbiology (N.R., S.B., L.A.), Uppsala University, SE-75123 Uppsala, Sweden; Department of Animal Breeding and Genetics (L.A.), Swedish University of Agricultural Sciences, SE-75007 Uppsala, Sweden; and Department of Veterinary Integrative Biosciences (L.A.), College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas 77843-4458
| | - Susanne Bornelöv
- Agricultural Research Organization (E.S., Y.C., S.Y., O.G., J.G.-S., M.F.-E.), Volcani Center, 50250 Bet-Dagan, Israel; Department of Medical Biochemistry and Microbiology (N.R., S.B., L.A.), Uppsala University, SE-75123 Uppsala, Sweden; Department of Animal Breeding and Genetics (L.A.), Swedish University of Agricultural Sciences, SE-75007 Uppsala, Sweden; and Department of Veterinary Integrative Biosciences (L.A.), College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas 77843-4458
| | - Leif Andersson
- Agricultural Research Organization (E.S., Y.C., S.Y., O.G., J.G.-S., M.F.-E.), Volcani Center, 50250 Bet-Dagan, Israel; Department of Medical Biochemistry and Microbiology (N.R., S.B., L.A.), Uppsala University, SE-75123 Uppsala, Sweden; Department of Animal Breeding and Genetics (L.A.), Swedish University of Agricultural Sciences, SE-75007 Uppsala, Sweden; and Department of Veterinary Integrative Biosciences (L.A.), College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas 77843-4458
| | - Miriam Friedman-Einat
- Agricultural Research Organization (E.S., Y.C., S.Y., O.G., J.G.-S., M.F.-E.), Volcani Center, 50250 Bet-Dagan, Israel; Department of Medical Biochemistry and Microbiology (N.R., S.B., L.A.), Uppsala University, SE-75123 Uppsala, Sweden; Department of Animal Breeding and Genetics (L.A.), Swedish University of Agricultural Sciences, SE-75007 Uppsala, Sweden; and Department of Veterinary Integrative Biosciences (L.A.), College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas 77843-4458
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ALPER M, TOKAY E, KÖÇKAR F. Amplification of GC-rich ADAMTS-2 and URG4/URGCP promoter regions with optimized combination of PCR enhancers. Turk J Biol 2016. [DOI: 10.3906/biy-1502-37] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
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Stefanska A, Gaffke L, Kaczorowska AK, Plotka M, Dabrowski S, Kaczorowski T. Highly thermostable RadA protein from the archaeon Pyrococcus woesei enhances specificity of simplex and multiplex PCR assays. J Appl Genet 2015; 57:239-49. [PMID: 26337425 DOI: 10.1007/s13353-015-0314-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2015] [Revised: 08/13/2015] [Accepted: 08/18/2015] [Indexed: 10/23/2022]
Abstract
The radA gene of the hyperthermophilic archaeon Pyrococcus woesei (Thermococcales) was cloned and overexpressed in Escherichia coli. The 1050-bp gene codes for a 349-amino-acid polypeptide with an M r of 38,397 which shows 100 % positional amino acid identity to Pyrococcus furiosus RadA and 27.1 % to the E. coli RecA protein. Recombinant RadA was overproduced in Escherichia coli as a His-tagged fusion protein and purified to electrophoretic homogeneity using a simple procedure consisting of ammonium sulfate precipitation and metal-affinity chromatography. In solution RadA exists as an undecamer (11-mer). The protein binds both to ssDNA and dsDNA. RadA has been found to be highly thermostable, it remains almost unaffected by a 4-h incubation at 94 °C. The addition of the RadA protein to either simplex or multiplex PCR assays, significantly improves the specificity of DNA amplification by eliminating non-specific products. Among applications tested the RadA protein proved to be useful in allelic discrimination assay of HADHA gene associated with long-chain 3-hydroxylacyl-CoA dehydrogenase deficiency that in infancy may lead to hypotonia, serious heart and liver problems and even sudden death.
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Affiliation(s)
- Aleksandra Stefanska
- Department of Microbiology, University of Gdansk, Wita Stwosza 59, 80-308, Gdansk, Poland
| | - Lidia Gaffke
- Department of Microbiology, University of Gdansk, Wita Stwosza 59, 80-308, Gdansk, Poland
| | - Anna-Karina Kaczorowska
- Collection of Plasmids and Microorganisms, University of Gdansk, Wita Stwosza 59, 80-308, Gdansk, Poland
| | - Magdalena Plotka
- Department of Microbiology, University of Gdansk, Wita Stwosza 59, 80-308, Gdansk, Poland
| | | | - Tadeusz Kaczorowski
- Department of Microbiology, University of Gdansk, Wita Stwosza 59, 80-308, Gdansk, Poland.
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30
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Okolie CE, Wooldridge KG, Turner DP, Cockayne A, James R. Development of a new pentaplex real-time PCR assay for the identification of poly-microbial specimens containing Staphylococcus aureus and other staphylococci, with simultaneous detection of staphylococcal virulence and methicillin resistance markers. Mol Cell Probes 2015; 29:144-50. [DOI: 10.1016/j.mcp.2015.03.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Revised: 02/22/2015] [Accepted: 03/06/2015] [Indexed: 11/29/2022]
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31
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From the field to the lab: best practices for field preservation of bat specimens for molecular analyses. PLoS One 2015; 10:e0118994. [PMID: 25798819 PMCID: PMC4370412 DOI: 10.1371/journal.pone.0118994] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2014] [Accepted: 12/18/2014] [Indexed: 11/19/2022] Open
Abstract
Studies in molecular ecology depend on field-collected samples for genetic information, and the tissue sampled and preservation conditions strongly affect the quality of the DNA obtained. DNA yields from different tissue types have seldom been compared, and the relative performance of storage media has never been directly tested, even though these media may influence DNA degradation under field conditions. We analyzed DNA yield from buccal swabs and wing punches harvested from live bats using nucleic acid quantification as well as quantitative PCR for a single-copy nuclear locus. We also compared DNA yields from wing tissue preserved in three media: ethanol, NaCl-saturated dimethyl sulfoxide (DMSO), and silica desiccant. Wing punches yielded more total DNA than did buccal swabs, and wing tissues preserved in silica beads yielded significantly more total and nuclear DNA than those preserved in DMSO or ethanol. These results show that tissue type and preservation media strongly influence the quantity of DNA obtained from non-lethal genetic samples, and based on these effects we provide recommendations for field collection of tissues for genetic analyses.
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Abstract
Whole genome amplification (WGA) is a widely used molecular technique that is becoming increasingly necessary in genetic research on a range of sample types including individual cells, fossilized remains and entire ecosystems. Multiple methods of WGA have been developed, each with specific strengths and weaknesses, but with a common defect in that each method distorts the initial template DNA during the course of amplification. The type, extent, and circumstance of the bias vary with the WGA method and particulars of the template DNA. In this review, we endeavor to discuss the types of bias introduced, the susceptibility of common WGA techniques to these bias types, and the interdependence between bias and characteristics of the template DNA. Finally, we attempt to illustrate some of the criteria specific to the analytical platform and research application that should be considered to enable combination of the appropriate WGA method, template DNA, sequencing platform, and intended use for optimal results.
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Affiliation(s)
| | - John H Leamon
- CyVek Inc., 2 Barnes Industrial Road South, Wallingford, CT, 06492, USA.
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PCR amplification of repetitive DNA: a limitation to genome editing technologies and many other applications. Sci Rep 2014; 4:5052. [PMID: 24852006 PMCID: PMC4031481 DOI: 10.1038/srep05052] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2014] [Accepted: 05/06/2014] [Indexed: 11/08/2022] Open
Abstract
Designer transcription-activator like effectors (TALEs) is a promising technology and made it possible to edit genomes with higher specificity. Such specific engineering and gene regulation technologies are also being developed using RNA-binding proteins like PUFs and PPRs. The main feature of TALEs, PUFs and PPRs is their repetitive DNA/RNA-binding domains which have single nucleotide binding specificity. Available kits today allow researchers to assemble these repetitive domains in any combination they desire when generating TALEs for gene targeting and editing. However, PCR amplifications of such repetitive DNAs are highly problematic as these mostly fail, generating undesired artifact products or deletions. Here we describe the molecular mechanisms leading to these artifacts. We tested our models also in plasmid templates containing one copy versus two copies of GFP-coding sequence arranged as either direct or inverted repeats. Some limited solutions in amplifying repetitive DNA regions are described.
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Marshall PL, King JL, Budowle B. Utility of amplification enhancers in low copy number DNA analysis. Int J Legal Med 2014; 129:43-52. [PMID: 24848516 DOI: 10.1007/s00414-014-1021-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2014] [Accepted: 05/05/2014] [Indexed: 11/26/2022]
Abstract
One parameter that impacts the robustness and reliability of forensic DNA analyses is the amount of template DNA used in the polymerase chain reaction (PCR). With short tandem repeat (STR) typing, low copy number (LCN) DNA samples can present exaggerated stochastic effects during the PCR that result in heterozygote peak height imbalance, allele drop out, and increased stutter. Despite these effects, there has been little progress toward decreasing the formation of stutter products and heterozygote peak imbalance effects during PCR. In an attempt to develop a more robust system that is less refractory to stochastic effects, the PCR additives, betaine, DMSO, PEG, and PCRboost®, were investigated on low-quantity DNA samples. The effects of the additives were assessed by evaluating STR typing results. Of the four additives, the only positive effects were observed with betaine treatment. Betaine, at a final concentration of 1.25 mol/L, was found to improve the robustness of the amplification, specifically by decreasing stutter in a dual locus system. In contrast, the addition of 1.25 mol/L betaine to commercial STR amplification kits did not affect stutter ratios. However, the addition of betaine did lead to increased yield of PCR products in all commercial kits tested. The results support that betaine can improve amplification efficiency of LCN DNA samples.
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Affiliation(s)
- Pamela L Marshall
- Institute of Applied Genetics, Department of Forensic and Investigative Genetics, University of North Texas Health Science Center, 3500 Camp Bowie Blvd, Fort Worth, TX, 76107, USA,
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Construction of a novel liver-targeting fusion interferon by incorporation of a Plasmodium region I-plus peptide. BIOMED RESEARCH INTERNATIONAL 2014; 2014:261631. [PMID: 24575402 PMCID: PMC3915749 DOI: 10.1155/2014/261631] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/01/2013] [Accepted: 09/12/2013] [Indexed: 01/12/2023]
Abstract
Interferon alpha (IFN α) exerts a multiplicity of biological actions including antiviral, immunomodulatory, and antiproliferative effects. Administration of IFN α is the current treatment for chronic hepatitis B; however, therapy outcome has not been completely satisfactory. The systemic effects of IFN α may account for its low in vivo biological activity and multiple adverse events. The purpose of this study was to design a novel liver-targeting fusion interferon (IFN-CSP) by fusing IFN α2b with a Plasmodium region I-plus peptide, thus targeting the drug specifically to the liver. The DNA sequence encoding IFN-CSP was constructed using improved splicing by overlapping extension-PCR method, and then cloned into the pET-21b vector for protein expression in E. coli BL21 (DE3). The recombinant protein was expressed as a His-tagged protein and purified using a combination of Ni affinity and HiTrap affinity chromatography at a purity of over 95%. The final yield of biologically active IFN-CSP was up to 270 mg/L culture. The purified recombinant protein showed anti-HBV activity and liver-targeting potentiality in vitro. These data suggests that the novel fusion interferon IFN-CSP may be an excellent candidate as a liver-targeting anti-HBV agent.
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36
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Tan MH, Gécz J, Shoubridge C. PCR amplification and sequence analysis of GC-rich sequences: Aristaless-related homeobox example. Methods Mol Biol 2014; 1017:105-20. [PMID: 23719911 DOI: 10.1007/978-1-62703-438-8_8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/13/2023]
Abstract
PCR amplification (followed by mutation scanning or direct sequencing) is a technique widely used in mutation detection and molecular studies of disease-causing genes, such as ARX. PCR amplification of high GC-rich regions encounters difficulties using conventional PCR procedures. Here, we present the strategies to amplify and sequence these GC-rich regions for the purposes of mutation screening and other molecular analyses.
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Affiliation(s)
- May H Tan
- Department of Paediatrics, University of Adelaide, Adelaide, SA, Australia
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Wu J, Kodzius R, Cao W, Wen W. Extraction, amplification and detection of DNA in microfluidic chip-based assays. Mikrochim Acta 2013. [DOI: 10.1007/s00604-013-1140-2] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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38
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Obradovic J, Jurisic V, Tosic N, Mrdjanovic J, Perin B, Pavlovic S, Djordjevic N. Optimization of PCR conditions for amplification of GC-Rich EGFR promoter sequence. J Clin Lab Anal 2013; 27:487-93. [PMID: 24218132 PMCID: PMC6807403 DOI: 10.1002/jcla.21632] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2013] [Accepted: 05/07/2013] [Indexed: 11/07/2022] Open
Abstract
BACKGROUND Polymerase chain reaction (PCR) is an extremely sensitive method that often demands optimization, especially when difficult templates need to be amplified. The aim of the present study was to optimize the PCR conditions for amplification of the epidermal growth factor receptor (EGFR) promoter sequence featuring an extremely high guanine-cytosine (GC) content in order to detect single nucleotide polymorphisms -216G>T and -191C>A. METHODS Genomic DNA used for amplification was extracted from formalin-fixed paraffin-embedded lung tumor tissue and PCR products were detected by agarose gel electrophoresis. RESULTS Results showed that addition of 5% dimethyl sulfoxide (DMSO), as well as DNA concentration in PCR reaction of at least 2 μg/ml, were necessary for successful amplification. Due to high GC content, optimal annealing temperature was 7°C higher than calculated, while adequate MgCl2 concentration ranged from 1.5 to 2.0 mM. CONCLUSION In conclusion, EGFR promoter region is a difficult PCR target, but it could be amplified after optimization of MgCl2 concentration and annealing temperature in the presence of DMSO and the DNA template of acceptable concentration.
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Affiliation(s)
- Jasmina Obradovic
- Faculty of Medical SciencesUniversity of KragujevacKragujevacSerbia
- Faculty of ScienceInstitute of Biology and EcologyUniversity of KragujevacKragujevacSerbia
| | - Vladimir Jurisic
- Faculty of Medical SciencesUniversity of KragujevacKragujevacSerbia
| | - Natasa Tosic
- Institute of Molecular Genetics and Genetic EngineeringUniversity of BelgradeBelgradeSerbia
| | - Jasminka Mrdjanovic
- Oncology Institute of Vojvodina, Faculty of Medicine, University of Novi SadSremska KamenicaSerbia
| | - Branislav Perin
- Institute for Pulmonary Diseases of VojvodinaClinic for Pulmonary OncologyFaculty of MedicineUniversity of Novi SadSremska KamenicaSerbia
| | - Sonja Pavlovic
- Institute of Molecular Genetics and Genetic EngineeringUniversity of BelgradeBelgradeSerbia
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Thanh T, Chi VTQ, Abdullah MP, Omar H, Napis S. Efficiency of ligation-mediated PCR and TAIL-PCR methods for isolation of RbcS promoter sequences from green microalga Ankistrodesmus convolutus. Mol Biol 2012. [DOI: 10.1134/s0026893312010220] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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40
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Madeira da Silva L, Vandepas L, Bianco SDC. Mutagenesis and analysis of genetic mutations in the GC-rich KISS1 receptor sequence identified in humans with reproductive disorders. J Vis Exp 2011:e2897. [PMID: 21912371 DOI: 10.3791/2897] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
The kisspeptin receptor (KISS1R) is a G protein-coupled receptor recognized as the trigger of puberty and a regulator of reproductive competence in adulthood (1,2,3). Inactivating mutations in KISS1R identified in patients have been associated with iodiopathic hypogonadotropic hypogonadism (IHH) (1,2) and precocious puberty (4). Functional studies of these mutants are crucial for our understanding of the mechanisms underlying the regulation of reproduction by this receptor as well as those shaping the disease outcomes, which result from abnormal KISS1R signaling and function. However, the highly GC-rich sequence of the KISS1R gene makes it rather difficult to introduce mutations or amplify the gene encoding this receptor by PCR. Here we describe a method to introduce mutations of interest into this highly GC-rich sequence that has been used successfully to generate over a dozen KISS1R mutants in our laboratory. We have optimized the PCR conditions to facilitate the amplification of a range of KISS1R mutants that include substitutions, deletions or insertions in the KISS1R sequence. The addition of a PCR enhancer solution, as well as of a small percentage of DMSO were especially helpful to improve amplification. This optimized procedure may be useful for other GC-rich templates as well. The expression vector encoding the KISS1R is been used to characterize signaling and function of this receptor in order to understand how mutations may change KISS1R function and lead to the associated reproductive phenotypes. Accordingly, potential applications of KISS1R mutants generated by site-directed mutagenesis can be illustrated by many studies (1,4,5,6,7,8). As an example, the gain-of-function mutation in the KISS1R (Arg386Pro), which is associated with precocious puberty, has been shown to prolong responsiveness of the receptor to ligand stimulation (4) as well as to alter the rate of degradation of KISS1R (9). Interestingly, our studies indicate that KISS1R is degraded by the proteasome, as opposed to the classic lysosomal degradation described for most G protein-coupled receptors (9). In the example presented here, degradation of the KISS1R is investigated in Human Embryonic Kidney Cells (HEK-293) transiently expressing Myc-tagged KISS1R (MycKISS1R) and treated with proteasome or lysosome inhibitors. Cell lysates are immunoprecipitated using an agarose-conjugated anti-myc antibody followed by western blot analysis. Detection and quantification of MycKISS1R on blots is performed using the LI-COR Odyssey Infrared System. This approach may be useful in the study of the degradation of other proteins of interest as well.
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Affiliation(s)
- Luciana Madeira da Silva
- Division of Endocrinology and Metabolism, Department of Medicine, University of Miami Miller School of Medicine, USA
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Development of a simple PCR-based assay for the identification of triazine resistance in the noxious plant common ragweed (Ambrosia artemisiifolia) and its applicability in higher plants. Biotechnol Lett 2011; 33:2509-15. [PMID: 21809088 DOI: 10.1007/s10529-011-0714-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2011] [Accepted: 07/20/2011] [Indexed: 10/17/2022]
Abstract
Bidirectional allele-specific PCR (Bi-PASA) was used to detect a point mutation causing triazine resistance in common ragweed (Ambrosia artemisiifolia). The external primers amplified a 278 bp standard DNA fragment in all genotypes. In the susceptible S264S genotypes, a 208 bp fragment was expected while in resistant S264G common ragweed genotypes a 109 bp band was expected. In resistant plants, both the wild and mutant type fragments were detected, indicating that the original triazine sensitive cpDNA is maintained in a heteroplasmic state in the resistant S264G genotypes. Additionally, in silico analysis confirmed the potential applicability of our diagnostic assay for other plant species. In 24 out of 74 taxa (32%), the assay could be used without any change, while in the others some of the primers should be redesigned before use.
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42
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Sequencing of high G+C microbial genomes using the ultrafast pyrosequencing technology. J Biotechnol 2011; 155:68-77. [DOI: 10.1016/j.jbiotec.2011.04.010] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2011] [Revised: 03/30/2011] [Accepted: 04/11/2011] [Indexed: 11/17/2022]
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An efficient and rapid method for cDNA cloning from difficult templates using codon optimization and SOE-PCR: with human RANK and TIMP2 gene as examples. Biotechnol Lett 2011; 33:1939-47. [PMID: 21660576 DOI: 10.1007/s10529-011-0656-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2011] [Accepted: 05/26/2011] [Indexed: 10/18/2022]
Abstract
As gene cloning from difficult templates with regionalized high GC content is a long recognized problem, we have developed a novel and reliable method to clone such genes. Firstly, the high GC content region of the target cDNA was synthesized directly after codon optimization and the remaining cDNA fragment without high GC content was generated by routine RT-PCR. Then the entire redesigned coding sequence of the target gene was obtained by fusing the above available two cDNA fragments with SOE-PCR (splicing by overlapping extension-PCR). We have cloned the human RANK gene (ten exons; CDS 1851 bp) using this strategy. The redesigned cDNA was transfected into an eukaryotic expression system (A459 cells) to verify its expression. RT-PCR and western blotting confirmed this. To validate our method, we also successfully cloned human TIMP2 gene (five exons; CDS 660 bp) also having a regionalized high GC content. Our strategy for combining codon optimization and SOE-PCR to clone difficult genes is thus feasible and potentially universally applicable.
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Li LY, Li Q, Yu YH, Zhong M, Yang L, Wu QH, Qiu YR, Luo SQ. A primer design strategy for PCR amplification of GC-rich DNA sequences. Clin Biochem 2011; 44:692-8. [PMID: 21315705 DOI: 10.1016/j.clinbiochem.2011.02.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2010] [Revised: 12/20/2010] [Accepted: 02/01/2011] [Indexed: 10/18/2022]
Abstract
OBJECTIVES To establish a primer design method for amplification of GC-rich DNA sequences. DESIGN AND METHODS A group of 15 pairs of primers with higher T(m) (>79.7°C) and lower level ΔT(m) (<1°C) were designed to amplify GC-rich sequences (66.0%-84.0%). The statistical analysis of primer parameters and GC content of PCR products was performed and compared with literatures. Other control experiments were conducted using shortened primers for GC-rich PCR amplifications in this study, and the statistical analysis of shortened primer parameters and GC content of PCR products was performed compared with primers not shortened. A group of 26 pairs of primers were designed to test the applicability of this primer designing strategy in amplifications of non-GC-rich sequences (35.2%-53.5%). RESULTS All the DNA sequences in this study were successfully amplified. Statistical analyses show that the T(m) and ΔT(m) were the main factors influencing amplifications. CONCLUSIONS This primer designing strategy offered a perfect tool for amplification of GC-rich sequences. It proves that the secondary structures cannot be formed at higher annealing temperature conditions (>65°C), and we can overcome this difficulty easily by designing primers and using higher annealing temperature.
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Affiliation(s)
- Li-Yan Li
- Department of Cytobiology, Southern Medical University, Guangzhou 510515, PR China
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Ma J, Wang PW, Yao D, Wang YP, Yan W, Guan SC. Single-primer PCR correction: a strategy for false-positive exclusion. GENETICS AND MOLECULAR RESEARCH 2011; 10:150-9. [PMID: 21308656 DOI: 10.4238/vol10-1gmr988] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Polymerase chain reaction (PCR) technology plays an important role in molecular biology research, but false-positive and nonspecific PCR amplification have plagued many researchers. Currently, research on the optimization of the PCR system focuses on double-primer-based PCR products. This research has shown that PCR amplification based on single-primer binding to the DNA template is an important contributing factor to obtaining false-positive results, fragment impurity, and nonspecific fragment amplification, when the PCR conditions are highly restricted during PCR-based target gene cloning, detection of transgenic plants, simple-sequence repeat marker-assisted selection, and mRNA differential display. Here, we compared single- and double-primer amplification and proposed "single-primer PCR correction"; improvements in PCR that eliminate interference caused by single-primer-based nonspecific PCR amplification were demonstrated and the precision and success rates of experiments were increased. Although for some kinds of experiments, the improvement effect of single-primer PCR correction was variable, the precision and success rate could be elevated at 12-50% in our experiment by this way.
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Affiliation(s)
- J Ma
- Biotechnology Center of Jilin Agricultural University, Changchun, PR China
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46
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Tiwari P, Saini S, Upmanyu S, Benjamin B, Tandon R, Saini KS, Sahdev S. Enhanced expression of recombinant proteins utilizing a modified baculovirus expression vector. Mol Biotechnol 2010; 46:80-9. [PMID: 20424933 DOI: 10.1007/s12033-010-9284-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
The baculovirus expression vector system (BEVS) has been widely used for over-expressing eukaryotic proteins due to a close resemblance in post-translational modification, processing, and transportation properties of the expressed protein, to that of the mammalian cells. In comparison to the bacterial expression system, protein yield from BEVS is relatively low, resulting in higher cost of production. To improve the existing recombinant protein expression levels, baculovirus homologous region1 (hr1) was strategically integrated into the bacmid-based transfer vectors. Luciferase reporter, human Protein Kinase B-alpha (PKB-A), and N-terminal-modified CYP-1A2 genes were independently cloned in non-hr1 and hr1 constructs for generating respective bacmids and baculoviruses. These recombinant baculoviruses were utilized for comparing the expression levels at varying multiplicity of infections (MOI) and time intervals in Spodoptera frugiperda (Sf21) or Trichoplusia ni (Tni) insect cell lines. Targeted insertion of hr1 upstream to CYP-1A2, PKB-A, and Luciferase genes, compared to the non-hr1 sets, led to 3-, 3.5-, and 4.5-fold increase in the resultant protein levels, respectively. Moreover, at equal protein concentration, the corresponding activity and inhibition characteristics of these high expression hr1 sets were comparable to that of the respective non-hr1 sets. Utilization of this modified baculovirus expression construct offers significant advantage of producing recombinant proteins in a cost-effective manner for various biotechnological and therapeutic applications.
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Affiliation(s)
- Prabhakar Tiwari
- Department of Molecular Technology, New Drug Discovery Research, Ranbaxy Research Laboratories-R&D-3, 20-Sector 18 Udyog Vihar, Gurgaon, India.
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47
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Wei M, Deng J, Feng K, Yu B, Chen Y. Universal method facilitating the amplification of extremely GC-rich DNA fragments from genomic DNA. Anal Chem 2010; 82:6303-7. [PMID: 20565067 DOI: 10.1021/ac100797t] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Polymerase chain reaction (PCR) is a basic technique with wide applications in molecular biology. Despite the development of different methods with various modifications, the amplification of GC-rich DNA fragments is frequently troublesome due to the formation of complex secondary structure and poor denaturation. Given the fact that GC-rich genes are closely related to transcriptional regulation, transcriptional silencing, and disease progression, we developed a PCR method combining a stepwise procedure and a mixture of additives in the present work. Our study demonstrated that the PCR method could successfully amplify targeted DNA fragments up to 1.2 Kb with GC content as high as 83.5% from different species. Compared to all currently available methods, our work showed satisfactory, adaptable, fast and efficient (SAFE) results on the amplification of GC-rich targets, which provides a versatile and valuable tool for the diagnosis of genetic disorders and for the study of functions and regulations of various genes.
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Affiliation(s)
- Maochen Wei
- Laboratory of Chemical Biology, China Pharmaceutical University, Nanjing, People's Republic of China
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48
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Shinoda N, Yoshida T, Kusama T, Takagi M, Hayakawa T, Onodera T, Sugiura K. High GC contents of primer 5'-end increases reaction efficiency in polymerase chain reaction. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2010; 28:324-30. [PMID: 20183585 DOI: 10.1080/15257770902963400] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Many studies have suggested that regulation of the polymerase chain reaction (PCR) is influenced by several factors. However, the understanding of reaction efficiency factors is not sufficient. Here we propose that high GC contents of primer 5'-end increases reaction efficiency in PCR. Using 71 primers (45 pairs), we analyzed factors that affect reaction efficiency, and statistically tested the correlation between the amplification signals and several factors. As a result, there were significant correlations between the amplification signals and the GC contents in the first 1 approximately 3 bps of primer 5'-end.
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Affiliation(s)
- Naoki Shinoda
- Food and Agricultural Materials Inspection Center, Saitama, Japan.
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DMSO and betaine greatly improve amplification of GC-rich constructs in de novo synthesis. PLoS One 2010; 5:e11024. [PMID: 20552011 PMCID: PMC2883997 DOI: 10.1371/journal.pone.0011024] [Citation(s) in RCA: 86] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2010] [Accepted: 05/16/2010] [Indexed: 01/10/2023] Open
Abstract
In Synthetic Biology, de novo synthesis of GC-rich constructs poses a major challenge because of secondary structure formation and mispriming. While there are many web-based tools for codon optimizing difficult regions, no method currently exists that allows for potentially phenotypically important sequence conservation. Therefore, to overcome these limitations in researching GC-rich genes and their non-coding elements, we explored the use of DMSO and betaine in two conventional methods of assembly and amplification. For this study, we compared the polymerase (PCA) and ligase-based (LCR) methods for construction of two GC-rich gene fragments implicated in tumorigenesis, IGF2R and BRAF. Though we found no benefit in employing either DMSO or betaine during the assembly steps, both additives greatly improved target product specificity and yield during PCR amplification. Of the methods tested, LCR assembly proved far superior to PCA, generating a much more stable template to amplify from. We further report that DMSO and betaine are highly compatible with all other reaction components of gene synthesis and do not require any additional protocol modifications. Furthermore, we believe either additive will allow for the production of a wide variety of GC-rich gene constructs without the need for expensive and time-consuming sample extraction and purification prior to downstream application.
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Abstract
Amplification of GC-rich DNA sequences is still a difficult task worldwide. Two frequently seen and inexpensive reagents—ethylene glycol and 1,2-propanediol—were found to be more effective than betaine in the amplification of 104 randomly selected GC-rich human DNA sequences with GC contents of 60–80% and lengths of 700–800 bp.
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